Merge branch 'benefit_from_validator' into 'master'

benefit from validator and improve tests

See merge request !81

nxtomomill/app/test/test_patch_nx_app.py

@@ -54,8 +54,8 @@ def test_patch_nx_application():
             n_proj=nproj,
             n_ini_proj=nproj,
             create_ini_dark=False,
-            create_ini_ref=False,
-            create_final_ref=False,
+            create_ini_flat=False,
+            create_final_flat=False,
             dim=dim,
         ).scan
         main(

nxtomomill/converter/dxfile/test_dxfile.py

@@ -37,6 +37,7 @@ from nxtomomill import converter
 from tomoscan.esrf.hdf5scan import HDF5TomoScan
 from nxtomomill.test.utils.dxfile import MockDxFile
 from silx.io.utils import get_data
+from tomoscan.validator import is_valid_for_reconstruction
 
 
 class TestDxToNxConverter(unittest.TestCase):
@@ -83,6 +84,7 @@ class TestDxToNxConverter(unittest.TestCase):
                 self.assertEqual(len(scan.flats), self.n_flats)
                 self.assertEqual(numpy.array(scan.rotation_angle).min(), 0)
                 self.assertEqual(numpy.array(scan.rotation_angle).max(), 180)
+                assert is_valid_for_reconstruction(scan)
 
                 # check arrays are correctly copied from mock
                 numpy.testing.assert_array_equal(

nxtomomill/converter/edf/test/test_edf2nx.py

@@ -36,6 +36,7 @@ from tomoscan.esrf.mock import MockEDF
 from tomoscan.esrf.hdf5scan import HDF5TomoScan
 from tomoscan.esrf.edfscan import EDFTomoScan
 from tomoscan import version
+from tomoscan.validator import is_valid_for_reconstruction
 from nxtomomill.utils import Progress
 import pytest
 
@@ -75,3 +76,4 @@ def test_edf_to_nx_converter(progress):
         assert len(hdf5_scan.alignment_projections) == n_alignment_proj
         assert hdf5_scan.dim_1 == dim
         assert hdf5_scan.dim_2 == dim
+        assert is_valid_for_reconstruction(hdf5_scan)

nxtomomill/converter/hdf5/test/test_hdf5converter.py

@@ -41,6 +41,7 @@ from nxtomomill.converter.hdf5.acquisition.baseacquisition import EntryReader
 from nxtomomill.converter.hdf5.acquisition.baseacquisition import DatasetReader
 from nxtomomill.io.config import TomoHDF5Config
 from tomoscan.esrf.hdf5scan import HDF5TomoScan
+from tomoscan.validator import is_valid_for_reconstruction
 from nxtomomill.test.utils.bliss import MockBlissAcquisition
 from silx.io.url import DataUrl
 from silx.io.utils import get_data
@@ -70,11 +71,13 @@ def url_has_been_copied(file_path: str, url: DataUrl):
 
 class TestH5ToNxConverter(unittest.TestCase):
     def setUp(self) -> None:
+        super().setUp()
         self.folder = tempfile.mkdtemp()
         self.config = TomoHDF5Config()
 
     def tearDown(self) -> None:
         shutil.rmtree(self.folder)
+        super().tearDown()
 
     def test_simple_converter_with_nx_detector_attr(self):
         """
@@ -286,6 +289,7 @@ class TestH5ToNxConverter(unittest.TestCase):
             scan = HDF5TomoScan(scan=res_tuple[0], entry=res_tuple[1])
             if hasattr(scan, "z_translation"):
                 self.assertTrue(scan.z_translation is not None)
+            self.assertTrue(is_valid_for_reconstruction(scan))
 
     def test_ignore_sub_entries(self):
         """
@@ -389,12 +393,14 @@ class TestDetectorDetection(unittest.TestCase):
 
 class TestXRDCTConversion(unittest.TestCase):
     def setUp(self) -> None:
+        super().setUp()
         self.folder = tempfile.mkdtemp()
         self.config = TomoHDF5Config()
         self.config.format = Format.XRD_CT
 
     def tearDown(self) -> None:
         shutil.rmtree(self.folder)
+        super().tearDown()
 
     def test_simple_converter_with_nx_detector_attr(self):
         """
@@ -442,6 +448,7 @@ class TestStandardAcqConversionWithExternalUrls(unittest.TestCase):
     """Test conversion when frames are provided from urls"""
 
     def setUp(self) -> None:
+        super().setUp()
         self.folder = tempfile.mkdtemp()
         self.config = TomoHDF5Config()
         self.config.output_file = os.path.join(self.folder, "output.nx")
@@ -468,6 +475,7 @@ class TestStandardAcqConversionWithExternalUrls(unittest.TestCase):
 
     def tearDown(self) -> None:
         shutil.rmtree(self.folder)
+        super().tearDown()
 
     def test_dataset_1(self):
         """test a conversion where projections are contained in the
@@ -497,18 +505,20 @@ class TestStandardAcqConversionWithExternalUrls(unittest.TestCase):
                 url=DataUrl(file_path=dark_flat_file, data_path="/3.1", scheme="silx"),
             ),
         )
-
         converter.from_h5_to_nx(
             configuration=self.config,
         )
 
-        self.assertTrue(os.path.exists(self.config.output_file))
+        self.assertTrue(
+            os.path.exists(self.config.output_file), "output file does not exists"
+        )
 
         with h5py.File(self.config.output_file, mode="r") as h5s:
             self.assertEqual(len(h5s.items()), 1)
             self.assertTrue("entry0000" in h5s)
 
         scan = HDF5TomoScan(scan=self.config.output_file, entry="entry0000")
+        self.assertTrue(is_valid_for_reconstruction(scan))
 
         # check the `data`has been created
         self.assertTrue(len(scan.projections), 20)
@@ -603,6 +613,7 @@ class TestStandardAcqConversionWithExternalUrls(unittest.TestCase):
                     self.assertEqual(vs.file_name, "acqui_1/sample_0/sample_0.h5")
 
         scan = HDF5TomoScan(scan=self.config.output_file, entry="entry0000")
+        self.assertTrue(is_valid_for_reconstruction(scan))
 
         # check the `data`has been created
         self.assertTrue(len(scan.projections), 40)
@@ -703,6 +714,7 @@ class TestZSeriesConversionWithExternalUrls(unittest.TestCase):
     """
 
     def setUp(self) -> None:
+        super().setUp()
         self.folder = tempfile.mkdtemp()
 
         self.config = TomoHDF5Config()
@@ -739,6 +751,7 @@ class TestZSeriesConversionWithExternalUrls(unittest.TestCase):
 
     def tearDown(self) -> None:
         shutil.rmtree(self.folder)
+        super().tearDown()
 
     def test_dataset_zseries(self):
         """Test a zseries with only external scan entries"""

nxtomomill/test/test_utils.py

@@ -58,8 +58,8 @@ class BaseTestAddDarkAndFlats(unittest.TestCase):
             n_proj=self.nproj,
             n_ini_proj=self.nproj,
             create_ini_dark=False,
-            create_ini_ref=False,
-            create_final_ref=False,
+            create_ini_flat=False,
+            create_final_flat=False,
             dim=self.dim,
         ).scan
         with h5py.File(self._simple_nx.master_file, mode="r") as h5s:
@@ -73,8 +73,8 @@ class BaseTestAddDarkAndFlats(unittest.TestCase):
             n_proj=0,
             n_ini_proj=0,
             create_ini_dark=False,
-            create_ini_ref=False,
-            create_final_ref=False,
+            create_ini_flat=False,
+            create_final_flat=False,
             dim=self.dim,
         ).scan
         self._create_vds(
@@ -94,8 +94,8 @@ class BaseTestAddDarkAndFlats(unittest.TestCase):
             n_proj=0,
             n_ini_proj=0,
             create_ini_dark=False,
-            create_ini_ref=False,
-            create_final_ref=False,
+            create_ini_flat=False,
+            create_final_flat=False,
             dim=self.dim,
         ).scan
         self._create_vds(
@@ -852,8 +852,8 @@ class TestChangeImageKeyControl(unittest.TestCase):
             n_proj=self.nproj,
             n_ini_proj=self.nproj,
             create_ini_dark=True,
-            create_ini_ref=True,
-            create_final_ref=True,
+            create_ini_flat=True,
+            create_final_flat=True,
             dim=self.dim,
             n_refs=4,
         )
@@ -1096,8 +1096,8 @@ class TestAddDarkAndFlatFromADifferentFolderWithVDS(unittest.TestCase):
             n_proj=10,
             n_ini_proj=2,
             create_ini_dark=False,
-            create_ini_ref=False,
-            create_final_ref=False,
+            create_ini_flat=False,
+            create_final_flat=False,
             dim=self.dim,
         ).scan
         # 1. add first level of indirection for dark and flat and check the VDS
@@ -1123,8 +1123,8 @@ class TestAddDarkAndFlatFromADifferentFolderWithVDS(unittest.TestCase):
             n_proj=10,
             n_ini_proj=2,
             create_ini_dark=False,
-            create_ini_ref=False,
-            create_final_ref=False,
+            create_ini_flat=False,
+            create_final_flat=False,
             dim=self.dim,
         ).scan
         # 2. create a second level of indirection for dark and flat and check